rs2711669

chr12-59735191-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001270623.2(SLC16A7):c.217+30173G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,070 control chromosomes in the GnomAD database, including 1,500 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1500 hom., cov: 33)
• Consequence: SLC16A7 NM_001270623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232

Genes affected

SLC16A7 (HGNC:10928): (solute carrier family 16 member 7) This gene is a member of the monocarboxylate transporter family. Members in this family transport metabolites, such as lactate, pyruvate, and ketone bodies. The protein encoded by this gene catalyzes the proton-linked transport of monocarboxylates and has the highest affinity for pyruvate. This protein has been reported to be more highly expressed in prostate and colorectal cancer specimens when compared to control specimens. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC16A7	NM_001270623.2	c.217+30173G>A		intron_variant		ENST00000547379.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC16A7	ENST00000547379.6	c.217+30173G>A		intron_variant		1	NM_001270623.2	P1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18658 AN: 151952 Hom.: 1496 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0797

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0869

Gnomad OTH AF: 0.115

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.123 AC: 18672 AN: 152070 Hom.: 1500 Cov.: 33 AF XY: 0.122 AC XY: 9039 AN XY: 74348

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.0795

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.0267

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.0528

Gnomad4 NFE AF: 0.0869

Gnomad4 OTH AF: 0.115

Alfa AF: 0.108 Hom.: 205

Bravo AF: 0.124

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.3
Dann	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2711669; hg19: chr12-60128972;